The S3 module for Media Mover just got updated to make the CDN integration easier. As files come through the system, files which already reside on S3 will have $file->s3_uri set which allows theming functions to display the local URI if it is present or the S3 URI if the file is already on S3.
Make that $file->s3_data which is a serialized array of data from the S3 file. This allows for the generation of private urls.